tbuckley/cabot-search huggingface dataset:
Wearable Devices: Implications for Precision Medicine and the Future of Health Care
Authors: Mohan Babu, Ziv Lautman, Xiangping Lin, Milan H.B. Sobota, Michael P. Snyder
Journal: Annual Review of Medicine (2023)

Wearable devices are integrated analytical units equipped with sensitive physical, chemical, and biological sensors capable of noninvasive and continuous monitoring of vital physiological parameters. Recent advances in disciplines including electronics, computation, and material science have resulted in affordable and highly sensitive wearable devices that are routinely used for tracking and managing health and well-being. Combined with longitudinal monitoring of physiological parameters, wearables are poised to transform the early detection, diagnosis, and treatment/management of a range of clinical conditions. Smartwatches are the most commonly used wearable devices and have already demonstrated valuable biomedical potential in detecting clinical conditions such as arrhythmias, Lyme disease, inflammation, and, more recently, COVID-19 infection. Despite significant clinical promise shown in research settings, there remain major hurdles in translating the medical uses of wearables to the clinic. There is a clear need for more effective collaboration among stakeholders, including users, data scientists, clinicians, payers, and governments, to improve device security, user privacy, data standardization, regulatory approval, and clinical validity. This review examines the potential of wearables to offer affordable and reliable measures of physiological status that are on par with FDA-approved specialized medical devices. We briefly examine studies where wearables proved critical for the early detection of acute and chronic clinical conditions with a particular focus on cardiovascular disease, viral infections, and mental health. Finally, we discuss current obstacles to the clinical implementation of wearables and provide perspectives on their potential to deliver increasingly personalized proactive health care across a wide variety of conditions.
Systematic comparison of rAAV vectors manufactured using large-scale suspension cultures of Sf9 and HEK293 cells
Authors: Shengjiang Liu, Jinzhong Li, Sameera Peraramelli, Ningguang Luo, Alan Chen, Minghua Dai, Fang Liu, Yanbao Yu, Ryan D. Leib, Ying Li, Kevin Lin, Derrick Huynh, Shuyi Li, Li Ou
Journal: Molecular Therapy (2023)
Improved Factor Combination for In Vivo Reprogramming of Cardiac Myofibroblast to Cardiomyocyte-Like Cell With Dual Recombinase Tracing
Authors: Jingdong Wu, Hong Zhao, Yanmeng Tao, Chunyan Yang, Yang Yang, Bin Zhou, Yang Zhao
Journal: Circulation (2023)

onrenewable cell types such as cardiomyocytes die with injury and aging, causing irreversible damage to normal heart function.In vivo direct reprogramming can promote heart regeneration by converting proliferative, extracellular matrix-secreting activated cardiac myofibroblasts into cardiomyocytes.This approach replenishes cardiomyocytes while simultaneously ameliorating cardiac fibrosis.Previous studies have reported in vivo cardiac fibroblast reprogramming into cardiomyocytes through the expression of transcription factors (such as GATA4, MEF2C, TBX5 [GMT]), microRNA silencing, or transcription factor expression in conjunction with small molecule activators. 1 However, our previous study showed that activated myofibroblasts, the ideal targets of in vivo cardiac reprogramming, are more difficult to reprogram than resident cardiac fibroblasts in vitro. 2 The efficiency remains unclear of in vivo cardiac myofibroblast-to-cardiomyocyte-like cell reprogramming using stringent lineage tracing systems.Furthermore, the discovery of genetic and chemical boosters of in vitro myofibroblast-to-cardiomyocyte reprogramming 2 (Tao Y,
More Tailored Approaches to Tuberculosis Treatment and Prevention
Authors: Charles M. Bark, W. Henry Boom, Jennifer J. Furin
Journal: Annual Review of Medicine (2023)

Recent advances in the treatment of tuberculosis (TB) have led to improvements unprecedented in our lifetime. Decades of research in developing new drugs, especially for multidrug-resistant TB, have created not only multiple new antituberculous agents but also a new approach to development and treatment, with a focus on maximizing the benefit to the individual patient. Prevention of TB disease has also been improved and recognized as a critical component of global TB control. While the momentum is positive, it will take continued investment at all levels, especially training of new dedicated TB researchers and advocates around the world, to maintain this progress.
Successful appendiceal incision by endoscopic submucosal dissection to allow endoscopic removal of an encapsulated fecalith
Authors: Qingyu Zeng, Zhang Tao, Jie Liu, Kong Tao, Xu Shan, Ya Lan Chen
Journal: Endoscopy (2023)

A 53-year-old man was admitted to our gastroenterology department for investigation of a colonic lump. Ultrasonic colonoscopy revealed a lump (about 0.8 cm) blocking the opening of the appendix and an encapsulated fecalith between the submucosa and the muscularis propria ([Fig. 1] and [Fig. 2] a). Removal of the encapsulated fecalith was difficult using only an endoscope. Therefore, the mucosa and submucosa were incised in the middle of the lump via endoscopic submucosal dissection (ESD); however, a scar was detected during the mucosal and submucosal incision ([Video 1]). The scar was incised with a DualKnife, subsequently revealing a hard yellow encapsulated fecalith ([Fig. 2] b). The lump had originated from inflammatory hyperplasia caused by the encapsulated fecalith. The encapsulated fecalith (about 1×1 cm) was removed using an endoscope ([Fig. 3]). Some bleeding at the incision site was detected endoscopically, and hemostatic clips were applied to stop this. Appendicography showed no residual encapsulated fecalith. The patient experienced slight abdominal distension at the end of the therapeutic endoscopy. He was discharged from the hospital 5 days later with no symptoms.
Laminin β4 is a constituent of the cutaneous basement membrane zone and additional autoantigen of anti-p200 pemphigoid
Authors: Stephanie Goletz, Manuela Pigors, Tina Rastegar Lari, Christoph M. Hammers, Yao Wang, Shirin Emtenani, Monique Aumailley, Maike M. Holtsche, Felix H. Stang, Imke Weyers, Inke R. König, Cristina Has, Christiane Radzimski, Lars Komorowski, Detlef Zillikens, Enno Schmidt
Journal: Journal of the American Academy of Dermatology (2023)

Background Anti-p200 pemphigoid is a subepidermal autoimmune blistering disease (AIBD) characterized by autoantibodies against a 200 kDa protein. Laminin γ1 has been described as target antigen in 70-90% of patients. No diagnostic assay is widely available for anti-p200 pemphigoid, which might be due to the unclear pathogenic relevance of anti-laminin γ1 autoantibodies. Objective To identify a target antigen with higher clinical and diagnostic relevance. Methods Immunoprecipitation, mass spectrometry, and immunoblotting were employed for analysis of skin extracts and sera of patients with anti-p200 pemphigoid (n=60), other AIBD (n=33), and healthy blood donors (n=29). To localize the new antigen in skin, cultured keratinocytes and fibroblasts, quantitative real-time PCR and immunofluorescence microscopy were performed. Results Laminin β4 was identified as target antigen of anti-p200 pemphigoid in all analyzed patients. It was located at the level of the basement membrane zone of the skin with predominant expression in keratinocytes. Limitations A higher number of sera needs to be tested to verify that laminin β4 is the diagnostically relevant antigen of anti-p200 pemphigoid. Conclusion The identification of laminin β4 as an additional target antigen in anti-p200 pemphigoid will allow its differentiation from other AIBD and as such, improve the management of these rare disorders.
Effects of Mirikizumab on Histologic Resolution of Crohn's Disease in a Randomized Controlled Phase 2 Trial
Authors: Fernando Magro, Marijana Protic, Gert De Hertogh, Lai Shan Chan, Paul Pollack, Vipul Jairath, Hilde Carlier, Emily Hon, Brian G. Feagan, Noam Harpaz, Rish Pai, Walter Reinisch
Journal: Clinical Gastroenterology and Hepatology (2023)

Histologic evaluation of mucosal healing in Crohn's disease is an evolving treatment target. We evaluated histologic outcomes for mirikizumab efficacy and associations with endoscopic and 1-year outcomes.
Atrioventricular Block: Does This Patient Require a Pacemaker?
Authors: Esteban González-Torrecilla, Raquel Luna López, Pablo Ávila Alonso
Journal: Circulation (2023)

A 71-year-old woman was admitted due to intermittent palpitations and occasional episodes of mild dizziness, particularly noticeable on assuming a standing position during the past month.The ECG recorded in the emergency room is depicted in Figure 1.These ob-served sequences were repetitive for long periods during ECG monitoring.The patient's cardiovascular history and physical examination yielded no noteworthy findings.The echocardiogram did not reveal any significant structural abnormalities.Does this patient need a pacemaker?Please turn the page to read the diagnosis.
Differences in injury and concussion rates in a cohort of Canadian female and male youth Rugby Union: a step towards targeted prevention strategies
Authors: Isla J Shill, Stephen W West, Stacy Sick, Kathryn J Schneider, J Preston Wiley, Brent E Hagel, Amanda M Black, Carolyn A Emery
Journal: British Journal of Sports Medicine (2023)

To examine differences in match and training musculoskeletal injury and concussion rates and describe mechanisms of concussion while considering previous playing experience in female and male Canadian high school Rugby Union ('rugby') players.A 2-year prospective cohort study was completed in a high school league (n=361 females, 421 player-seasons; n=429 males, 481 player-seasons) in Calgary, Canada over the 2018 and 2019 rugby playing seasons. Baseline testing was completed at the start of each season and injury surveillance and individual player participation through session attendance was documented to quantify individual-level player exposure hours. Injury incidence rates (IRs) and incidence rate ratios (IRRs) were calculated using Poisson regression, offset by player exposure hours and clustered by team.Overall match IR for females was 62% higher than males (overall IRR=1.62, 95% CI: 1.20 to 2.18) and the overall training IR was twice as high for females (overall IRR=2.15, 95% CI: 1.40 to 3.32). The female match concussion IR was 70% higher than the males (concussion IRR=1.70, 95% CI: 1.08 to 2.69). Females had a 75% greater tackle-related IR compared with males (IRR=1.75, 95% CI: 1.20 to 2.56). Additionally, female tacklers had a twofold greater rate of injury compared with male tacklers (IRR=2.17, 95% CI: 1.14 to 4.14). Previous playing experience was not associated with tackle-related injury or concussion IRs.The rate of injury and concussion was significantly higher in females within this Canadian high school cohort. These results emphasise the need for development, implementation and evaluation of female-specific injury and concussion prevention strategies to reduce injury and concussion in female youth rugby.
Alzheimer’s genes in microglia: a risk worth investigating
Authors: Ari Sudwarts, Gopal Thinakaran
Journal: Molecular Neurodegeneration (2023)

Abstract Despite expressing many key risk genes, the role of microglia in late-onset Alzheimer’s disease pathophysiology is somewhat ambiguous, with various phenotypes reported to be either harmful or protective. Herein, we review some key findings from clinical and animal model investigations, discussing the role of microglial genetics in mediating perturbations from homeostasis. We note that impairment to protective phenotypes may include prolonged or insufficient microglial activation, resulting in dysregulated metabolomic (notably lipid-related) processes, compounded by age-related inflexibility in dynamic responses. Insufficiencies of mouse genetics and aggressive transgenic modelling imply severe limitations in applying current methodologies for aetiological investigations. Despite the shortcomings, widely used amyloidosis and tauopathy models of the disease have proven invaluable in dissecting microglial functional responses to AD pathophysiology. Some recent advances have brought modelling tools closer to human genetics, increasing the validity of both aetiological and translational endeavours.
Facemap: a framework for modeling neural activity based on orofacial tracking
Authors: Atika Syeda, Lin Zhong, Renee Tung, Will Long, Marius Pachitariu, Carsen Stringer
Journal: Nature Neuroscience (2023)

Recent studies in mice have shown that orofacial behaviors drive a large fraction of neural activity across the brain. To understand the nature and function of these signals, we need better computational models to characterize the behaviors and relate them to neural activity. Here we developed Facemap, a framework consisting of a keypoint tracker and a deep neural network encoder for predicting neural activity. Our algorithm for tracking mouse orofacial behaviors was more accurate than existing pose estimation tools, while the processing speed was several times faster, making it a powerful tool for real-time experimental interventions. The Facemap tracker was easy to adapt to data from new labs, requiring as few as 10 annotated frames for near-optimal performance. We used the keypoints as inputs to a deep neural network which predicts the activity of ~50,000 simultaneously-recorded neurons and, in visual cortex, we doubled the amount of explained variance compared to previous methods. Using this model, we found that the neuronal activity clusters that were well predicted from behavior were more spatially spread out across cortex. We also found that the deep behavioral features from the model had stereotypical, sequential dynamics that were not reversible in time. In summary, Facemap provides a stepping stone toward understanding the function of the brain-wide neural signals and their relation to behavior.
TFEB–vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy
Authors: Baiping Wang, Heidi Martini-Stoica, Chuangye Qi, Tzu-Chiao Lu, Shuo Wang, Wen Xiong, Yanyan Qi, Yin Xu, Marco Sardiello, Hongjie Li, Hui Zheng
Journal: Nature Neuroscience (2023)
Looking at frailty and intrinsic capacity through a geroscience lens: the ICFSR &amp; Geroscience Task Force
Authors: Philipe de Souto Barreto, Yves Rolland, Luigi Ferrucci, Hidenori Arai, Heike Bischoff-Ferrari, Gustavo Duque, Roger A. Fielding, John R. Beard, John Muscedere, Felipe Sierra, Bruno Vellas, Nathan K. LeBrasseur
Journal: Nature Aging (2023)
Intake of Energy Drinks Before and During Pregnancy and Adverse Pregnancy Outcomes
Authors: Ming Ding, Andre O. Markon, Olivia E. Jones-Dominic, Alexandra C. Purdue-Smithe, Janet W. Rich-Edwards, Beverly J. Wolpert, Jorge E. Chavarro
Journal: JAMA Network Open (2023)

Consumption of energy drinks has increased drastically in recent years, particularly among young people. It is unknown whether intake of energy drinks is associated with health during pregnancy.
Multiomic analysis of cervical squamous cell carcinoma identifies cellular ecosystems with biological and clinical relevance
Authors: Junpeng Fan, Funian Lu, Tianyu Qin, Wenju Peng, Xucui Zhuang, Yinuo Li, Xin Hou, Zixuan Fang, Yunyi Yang, Ensong Guo, Bin Yang, Xi Li, Yu Fu, Xiaoyan Kang, Zimeng Wu, Lili Han, Gordon B. Mills, Xiangyi Ma, Kezhen Li, Peng Wu, Ding Ma, Gang Chen, Chaoyang Sun
Journal: Nature Genetics (2023)
We must harness the power of social and behavioural science against the growing pandemic of antimicrobial resistance
Authors: Miroslav Sirota, Katrine Bach Habersaat, Cornelia Betsch, Daniela Lejla Bonga, Aleksandra Borek, Anica Buckel, Robb Butler, Lucie Byrne-Davis, Mark Caudell, Esmita Charani, Mattis Geiger, Marina Gross, Jo Hart, Olga Kostopoulou, Eva M. Krockow, Tiina Likki, Danilo Lo Fo Wong, Ana P. Santana, Elisabeth D. C. Sievert, Andriana Theodoropoulou, Alistair Thorpe, Marta Wanat, Robert Böhm
Journal: Nature Human Behaviour (2023)
Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder
Authors: Andrew Dahl, Michael Thompson, Ulzee An, Morten Krebs, Vivek Appadurai, Richard Border, Silviu-Alin Bacanu, Thomas Werge, Jonathan Flint, Andrew J. Schork, Sriram Sankararaman, Kenneth S. Kendler, Na Cai
Journal: Nature Genetics (2023)

Abstract Biobanks often contain several phenotypes relevant to diseases such as major depressive disorder (MDD), with partly distinct genetic architectures. Researchers face complex tradeoffs between shallow (large sample size, low specificity/sensitivity) and deep (small sample size, high specificity/sensitivity) phenotypes, and the optimal choices are often unclear. Here we propose to integrate these phenotypes to combine the benefits of each. We use phenotype imputation to integrate information across hundreds of MDD-relevant phenotypes, which significantly increases genome-wide association study (GWAS) power and polygenic risk score (PRS) prediction accuracy of the deepest available MDD phenotype in UK Biobank, LifetimeMDD. We demonstrate that imputation preserves specificity in its genetic architecture using a novel PRS-based pleiotropy metric. We further find that integration via summary statistics also enhances GWAS power and PRS predictions, but can introduce nonspecific genetic effects depending on input. Our work provides a simple and scalable approach to improve genetic studies in large biobanks by integrating shallow and deep phenotypes.
Deep learning-based phenotype imputation on population-scale biobank data increases genetic discoveries
Authors: Ulzee An, Ali Pazokitoroudi, Marcus Alvarez, Lianyun Huang, Silviu Bacanu, Andrew J. Schork, Kenneth Kendler, Päivi Pajukanta, Jonathan Flint, Noah Zaitlen, Na Cai, Andy Dahl, Sriram Sankararaman
Journal: Nature Genetics (2023)

Abstract Biobanks that collect deep phenotypic and genomic data across many individuals have emerged as a key resource in human genetics. However, phenotypes in biobanks are often missing across many individuals, limiting their utility. We propose AutoComplete, a deep learning-based imputation method to impute or ‘fill-in’ missing phenotypes in population-scale biobank datasets. When applied to collections of phenotypes measured across ~300,000 individuals from the UK Biobank, AutoComplete substantially improved imputation accuracy over existing methods. On three traits with notable amounts of missingness, we show that AutoComplete yields imputed phenotypes that are genetically similar to the originally observed phenotypes while increasing the effective sample size by about twofold on average. Further, genome-wide association analyses on the resulting imputed phenotypes led to a substantial increase in the number of associated loci. Our results demonstrate the utility of deep learning-based phenotype imputation to increase power for genetic discoveries in existing biobank datasets.
Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health implications
Authors: Daniel F. Levey, Marco Galimberti, Joseph D. Deak, Frank R. Wendt, Arjun Bhattacharya, Dora Koller, Kelly M. Harrington, Rachel Quaden, Emma C. Johnson, Priya Gupta, Mahantesh Biradar, Max Lam, Megan Cooke, Veera M. Rajagopal, Stefany L. L. Empke, Hang Zhou, Yaira Z. Nunez, Henry R. Kranzler, Howard J. Edenberg, Arpana Agrawal, Jordan W. Smoller, Todd Lencz, David M. Hougaard, Anders D. Børglum, Ditte Demontis, J. Michael Gaziano, Michael J. Gandal, Renato Polimanti, Murray B. Stein, Joel Gelernter
Journal: Nature Genetics (2023)

Abstract As recreational use of cannabis is being decriminalized in many places and medical use widely sanctioned, there are growing concerns about increases in cannabis use disorder (CanUD), which is associated with numerous medical comorbidities. Here we performed a genome-wide association study of CanUD in the Million Veteran Program (MVP), followed by meta-analysis in 1,054,365 individuals ( n cases = 64,314) from four broad ancestries designated by the reference panel used for assignment (European n = 886,025, African n = 123,208, admixed American n = 38,289 and East Asian n = 6,843). Population-specific methods were applied to calculate single nucleotide polymorphism-based heritability within each ancestry. Statistically significant single nucleotide polymorphism-based heritability for CanUD was observed in all but the smallest population (East Asian). We discovered genome-wide significant loci unique to each ancestry: 22 in European, 2 each in African and East Asian, and 1 in admixed American ancestries. A genetically informed causal relationship analysis indicated a possible effect of genetic liability for CanUD on lung cancer risk, suggesting potential unanticipated future medical and psychiatric public health consequences that require further study to disentangle from other known risk factors such as cigarette smoking.
Multilevel Implementation Strategies for Adolescent Human Papillomavirus Vaccine Uptake
Authors: Lila J. Finney Rutten, Joan M. Griffin, Jennifer L. St. Sauver, Kathy MacLaughlin, Jessica D. Austin, Gregory Jenkins, Jeph Herrin, Robert M. Jacobson
Journal: JAMA Pediatrics (2023)

Despite availability of a safe and effective vaccine, an estimated 36 500 new cancers in the US result from human papillomavirus (HPV) annually. HPV vaccine uptake falls short of national public health goals and lags other adolescent vaccines.
Violaceous Nodules on the Right Leg and Foot
Authors: Tai-Li Chen, Hao-Kai Chuang, Chen-Yi Wu
Journal: JAMA (2023)

A patient with a history of bullous pemphigoid treated with oral prednisolone presented with multiple round, dark brown to violaceous-colored firm nodules on the right leg and 2 nodular masses with hemorrhagic crusts on the right foot. Complete blood cell count and creatinine and liver function test results were normal, and results of HIV antibody testing were negative. What is the diagnosis and what would you do next?
Contextualizing Depression in Pacific Islander Sexual and Gender Minority Youth—Location, History, and Culture
Authors: Nikki Apana, Nicole V. DeVille, Kekoa Taparra
Journal: JAMA Pediatrics (2023)

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Infertility and Risk of Autism Spectrum Disorder in Children
Authors: Maria P. Velez, Natalie Dayan, Jonas Shellenberger, Jessica Pudwell, Dia Kapoor, Simone N. Vigod, Joel G. Ray
Journal: JAMA Network Open (2023)

Previous studies on the risk of childhood autism spectrum disorder (ASD) following fertility treatment did not account for the infertility itself or the mediating effect of obstetrical and neonatal factors.